Toru Hanai/Reuters

TOKYO—Japan’s ruling coalition, headed by Prime Minister Shinzo Abe, has been mired in scandal for several weeks amid allegations Abe personally bent the law or broke it to benefit his political cronies and friends. Even a senior member of Abe’s own Liberal Democratic Party says, “There is nothing this administration wouldn’t do to crush its enemies and reward its pals.”

The story became national news on May 29 when a 28-year-old journalist named Shiori held a press conference at the Tokyo District Court as she sought to reopen the closed investigation into her case. In accordance with the wishes of her relatives, she has kept her family name out of the papers.

Shiori claims that on April 4, 2015, Yamaguchi, the journalist closest to Prime Minister Abe, and a former Washington, D.C., bureau chief for the Japanese television network TBS, raped her while she was unconscious at the Sheraton Miyako Hotel. She had dinner and drinks with him before losing consciousness.

She filed charges with the Tokyo Metropolitan Takanawa Police who investigated the case diligently and even obtained an arrest warrant for Yamaguchi, only to be stopped by an order from a high-ranking bureaucrat right as they were set to arrest him at Narita Airport.

Like a scene out of a movie, the detective who had at first reluctantly taken her case but had become her advocate told her over the phone, “He’s walking past us. I can’t do anything. I’ve got orders from way above. I’ve just been told I’m being taken off the case, as well. I’m sorry.”

It wasn’t a scene from a movie. That was exactly what happened.

And that is where the story takes a major political twist. It is not surprising that the opposition party and Japan’s media are reporting the possibility of a cover-up or, at a minimum, gross interference in the rape investigation.

It’s quite a cast of characters that show up in this human drama, and it may help to have a program to keep them straight.

The Alleged Victim—Shiori, whose calm anger and direct account of events the press has found more than compelling, and whose case may well have helped force the Japanese parliament to revise the country’s horribly antiquated laws on sexual assault.

The Alleged Rapist—The wiry Yamaguchi, taking the Bill Cosby approach, insists that he is innocent and anything that happened was consensual, even though there is ample proof that Shiori was only semi-conscious if, indeed, she was conscious at all. He is beloved not only by Prime Minister Abe, but also by Japan’s right wing for an infamous article he penned which appeared to dismiss the sufferings of “the comfort women” who were enslaved to sexually service Japanese soldiers during WWII.

Mr. Fixit—Cabinet Spokesman Yoshihide Suga is about as close to the prime minister as white on rice, as they say in some parts of the United States. Physically unprepossessing, he is famed for his sarcasm, quick wit, and ability to keep cool. Suga figures in this story, as in many others in Japanese politics, as a likely go-between. In appearance, he bears some resemblance to the plastic Troll dolls of yesteryear, and in his demeanor, especially in his brawls with the press, he is like the most formidable internet troll made flesh—rarely losing a battle or getting rattled. He is everything that Sean Spicer would like to be, and could give Steve Bannon a run for his money.

The Chief—Suga’s former secretary, Itaru Nakamura, is a gruff, chubby National Police Agency career bureaucrat, who sports a type of combover known here as the “barcode” haircut. He was the chief of the Tokyo Police Criminal Investigation Bureau at the time the arrest warrant was issued. He allegedly gave the orders to stop the arrest and personally intervened to stall or scuttle the investigation.

The Prime Minister—Shinzo Abe, 62 years old, is a proud man with a long memory and a short temper, lashing out at his critics with infamous ferocity. This is his second time serving as prime minister after he gave up the job in 2007 due to illness. Just before Abe quit, he communicated his plans to resign to... Yamaguchi, who delivered the scoop for his network, achieving a great measure of fame as an ace reporter with rock-solid ties to the prime minister.

Yamaguchi’s details of his close relationship with Abe are highlighted in the two books he has written about him, especially his magnum opus, Sori (Prime Minister), which monthly magazine CYZO characterized as “a book full of flattery for Abe” punctuated with “Yamaguchi boasting about his close relationships to the Prime Minister and those around him.” Of course, the trollish Suga also makes an appearance in the books.

The Police Chief, is not mentioned in Yamaguchi’s writings but he appears to be quite loyal to Mr. Fixit and to Abe as well. When a television commentator criticized Abe’s fatal handling of the abduction of the freelance journalist Kenji Goto, The Chief reportedly sent him a message saying, “You deserve 10,000 deaths.” Police officers who know The Chief, aka Detective Barcode, say he doesn’t mince words. Unlike Shiori or Mr. Fixit, he also does not do on-the-record press conferences and has not given a full explanation of how he became involved with the case and why he decided to step in.

Shiori allowed reporters to print her first name and let cameramen photograph her face at her press conference where she spoke about her ordeal. Her full statement is here.

Shiori is an average-sized Japanese woman, thin, and well-mannered. She has worked at large international news agencies and her English is good. She is currently working on a documentary about guerrillas in South America; she is no shrinking violet. And in Japan, where rape victims are expected to cry, break down, and fall apart—or simply pretend the rape never happened—her steely resolve has surprised many.

The odds were never in her favor. Until very recently, sexual assault victims had to file charges for an investigation to take place, Japan’s 90 percent male police force often discouraged victims from filing charges, and first-time offenders could get away with no jail time at all if they apologized and paid compensation. Even if there was an arrest made, prosecutors routinely dropped half of the cases.

Shiori explains her decision: “I wanted to use my full name, but my family was against it. I have to question this situation where victims cannot talk unless they hide their face, remain sad, weak, and believe they have to feel shame,” she said in an interview with The Daily Beast.

“I believe it was necessary for me to talk about the horror of rape and the massive impact it had on my life afterward,” she said. “I am now painfully aware of how much the legal and social system fails sex crime victims. For a long time in Japan, women who have been sexually assaulted blame themselves or are blamed by others. When I was about 10, I went to a public pool in a bikini my parents had bought for me—and was terrified when a man groped me in the pool. But when I told the adults, they told me, ‘It’s because you were wearing a sexy bikini.’ So I thought, oh it is my fault. I don’t think like that any more.”

Shiori said she had met Yamaguchi for dinner in Tokyo on April 3, 2015, to discuss his offer to find her work in the United States. Shiori said Yamaguchi took her to two restaurants where she remembers having a few drinks. Her last memory before she lost consciousness was of dizzily leaning against a water cooler, she said.

A taxi driver who drove the pair later that night said Shiori repeatedly asked to be dropped off at the nearest station, she said, but Yamaguchi instructed the driver to head to a hotel.

“According to the driver’s testimony, I wasn’t able to get out of the taxi on my own, so Mr. Yamaguchi had to carry me,” she said.

Footage from a security camera at the Sheraton Miyako Hotel showed Yamaguchi carrying her out of the taxi and into the hotel. The Daily Beast confirmed the content of the video with a police source who also said investigators spoke to eyewitnesses. The Daily Beast also talked to a third source who viewed the hotel security video and confirmed Shiori’s characterization of the footage.

Shiori said she tried to file a report with the police, but officers initially tried to discourage her, warning her it would ruin her career. Investigators finally accepted Shiori’s criminal complaint in late April after she convinced an officer to check security footage from the hotel. The officer retrieved the footage on April 15. After the detectives watched the footage, they agreed there were grounds for a criminal case.

The police then enthusiastically pursued the case. It should be noted, that Shukan Shincho, the weekly magazine initially reporting on these events was also able to verify the details of Shiori’s account with witnesses.

Police officers obtained an arrest warrant for Yamaguchi on suspicion of incapacitated rape and were waiting to arrest him at Narita Airport on June 8, 2015. But investigators never executed the warrant and instead let him walk away, Shiori said.

They had received last minute “orders from above,” an investigator told her on the phone. Police sources confirmed this with The Daily Beast.

The call to halt the arrest came directly from The Chief (Nakamura) who as mentioned previously, headed the investigative bureau of the Tokyo Metropolitan Police at the time.

When responding to the enquiries of the weekly magazine Shincho, The Chief, admitted he called off the arrest, but said Abe’s administration had nothing to do with his decision. “I made the decision, by myself, based on the details of the case,” he said before Shiori went public.

The Chief began his career as a bureaucrat in Japan’s National Police Agency, which oversees all police forces in the country but cannot conduct investigations or conduct arrests; it gives guidance. Thus NPA bureaucrats are usually dispatched to local police departments at an executive officer level and are referred to as kyaria (career guys) by other police who are local hires. They rarely stay in one prefecture for long and lack the street sense of cops who start at the bottom and work their way up. “They’re the police elite. They usually are more like politicians than police officers,” said one Saitama Prefecture detective. NPA bureaucrats often are temporarily transferred to other agencies as well, such as the Nuclear Regulation Authority. At the time of the rape investigation, The Chief had been temporarily transferred to the Tokyo Metropolitan Police Department.

It is highly irregular for a top-ranking official to stop an arrest warrant or interfere with a case at this level, say many police sources. Jiro Ono, former chief of the Kagoshima Police Headquarters and a former Upper House Member of the Parliament publicly commented. “An arrest for incapacitated rape is typically done based on the judgment of the head of the police department [in this case Takanawa Police] and for the chief of the Criminal Investigative Bureau to butt in and give orders I must say is extremely abnormal.”

The irregularity of how this case has been handled is one reason Shiori is now seeking a reversal of the prosecutor’s decision.

Even a current high-ranking officer in the National Police Agency was critical of the handling of the case, and commented under condition of anonymity: “When you consider Nakamura’s close relationship to Abe and Suga, and the case involves Abe’s closest friend in the media, Mr. Yamaguchi, Nakamura’s intervention in the case was completely inappropriate. It’s a conflict of interest and it gives the appearance of impropriety. To anyone, it might appear that Nakamura, in his position as the head of the investigative bureau, deliberately squashed an investigation to benefit the friend of his former boss, Suga. It’s disgraceful. I don’t know whether that was the case but the problem is that people may reasonably believe that’s exactly what happened. It’s not hard to see why. Here’s how it could happen. Yamaguchi asks Abe or Suga to intervene. One of them calls Nakamura. Loyal to his former boss, Nakamura scuttles the arrest warrant and the case. It doesn’t take a massive criminal conspiracy to make that happen. It just takes a few phone calls.”

When pressed to go on the record, the officer declined, sheepishly explaining the Abe administration just hinted that they will have the whistleblower in the Kake Gakuen case (a brewing scandal involving the licensing of a school) prosecuted for violations of the Civil Servants Act—releasing information gained on the job. “That will be the end of that bureaucrat’s career and possibly time in jail,” the officer said. “I could argue that I am sharing police common sense, not secret information. But even then, as in the case of the whistleblower, anyone who opposes Abe ends up not only having their career shortened but their reputation ruined. If I was retired, like Mr. Ono, I’d be happy to go on the record.”

Former Prime Minister Yukio Hatoyama, however, pulled no punches in his comment on the case. On the evening of May 31, he tweeted, “What is wrong with Japan’s media?...They have remained silent on the rape committed by former TBS bureau chief, Yamaguchi, who is an intimate friend of Prime Minister Abe. Nakamura, the Chief of Criminal Investigations for the Tokyo Metropolitan Police Department, buried the arrest warrant and Nakamura was the former personal secretary of Cabinet Minister Suga. Except for Tokyo Shimbun [the newspaper], no other media outlet will write about this. Has Japan’s media’s sold out their national [sense of] justice to the Cabinet Office?” Perhaps it was the brevity of Twitter that resulted in Mr. Hatoyama not adding “allegedly” in front of the rape accusation, but over 12,000 people appear to agree with his sentiment.

The burying of the arrest warrant is not the only puzzling thing in the investigation.

Following the aborted arrest, the lead investigator was taken off the case, the prosecutor handling Shiori’s case, prosecutor Mori, was changed out, and the case was moved from the jurisdiction of Takanawa Police Department to the Criminal Investigative Division One (Violent Crimes) of Tokyo Police Headquarters, where The Chief would have day-to-day access to the detectives handling the case. The newly appointed detectives urged Shiori to settle with Mr. Yamaguchi and drop charges. She did not agree. The police eventually filed papers against Mr. Yamaguchi with the Tokyo prosecutors, where the case languished for months, until the prosecutors eventually decided to drop all charges against Yamaguchi in July of 2016. They would only say there was not sufficient evidence to indict.

Mr. Fixit, as the Cabinet spokesman, told reporters at a regular press briefing this month he had nothing to do with police calling off Yamaguchi’s arrest and said he was not informed of the investigation. Because The Chief (Nakamura), who called off the arrest, once worked for him, it’s not surprising that even Japan’s media would go through the motions of questioning him.

“I do not know anything about the details [of the Shiori case],” he said gruffly.

Shiori’s news conference led to heated debate online, and supporters quickly set up advocacy groups for her on social media while others stood outside parliament in solidarity, holding placards bearing the hashtag #FightTogetherWithShiori.

Shiori also faced vitriol and criticism for going public. Critics took to social media to say that she was using the case to gain fame, while other commentators blamed opponents of the Abe administration for orchestrating her press conference. And of course, there were many comments that her shirt was too revealing, which for a large number of Japanese men, seems to discredit her allegations.

Shinji Takeda, the president of Tokyo Broadcasting System Television (TBS), told reporters at a recent briefing the company did receive inquiries from the police at the time of the investigation but Yamaguchi quit without discussing details of the case with his employer.

The public distrust and paranoia that the Abe administration’s heavy-handed political tactics have generated have elevated Shiori’s case to a subject of national debate, even in parliamentary sessions. Of course, the opposition party sees it as a political opportunity to cast light on the Machiavellian machinations of Abe and his cronies—but that doesn’t mean they’re wrong.

Even members of Abe’s own political party fear the allegations that Abe or Mr. Fixit interfered with a police investigation are true. An Upper House Member in the LDP told The Daily Beast, “Do I know that Abe or Suga blocked this investigation? I do not. Do I believe that they could or would? Yes, without a doubt. The admirable thing about Shinzo Abe and his spiritual doppelgänger Suga is their absolutely fierce loyalty to their friends—they would bend the law, break the law, or cover up a scandal for their bosom buddies. In Japan, that’s a virtue. Such loyalty from the Oyabun (father-figure) generates great loyalty from the Kobun (child-figures). They would also do the same outrageous things to crush an enemy or the enemy of their friend. They terrorize members of our own party who express opposition not just the media or the occasional principled bureaucrat. I also believe they are true patriots. The problem is, and sometimes we forget this, elected officials are supposed to serve the public not their cronies or their own self-interests. The fact that the incredibly cautious Japanese media is reporting this at all should tell you, or anyone who knows Japan, that there is a real problem here.”

On his public Facebook page, Yamaguchi has consistently denied all allegations saying, “I have not done anything that violates or touches upon the the law,” and has written a long rebuttal to Shiori’s allegations.

Prime Minister Shinzo Abe’s wife, Akie, “liked” his posts.

In an email responding to questions from The Daily Beast, Yamaguchi said, “I am not acquainted at all with Itaru Nakamura, the previous head of the investigative bureau at the National Police Agency. I have never met, spoken, nor made any acquaintance with him at any event. I do not have his contact information.”

He continued, “I have neither informed nor consulted with politicians, including Prime Minister Abe or Chief Cabinet Secretary Suga on this issue.” Yamaguchi insists that this is simply a matter between a male and female journalist and that there was nothing unusual about the investigation.

Yet, it is hard to see this as the case, because multiple police sources assert that if Yamaguchi was not a famous journalist or a friend of the prime minister, he would have been arrested and subject to 23 days of interrogation without a lawyer present, just like most suspects in Japan. The Japanese criminal justice system itself is incredibly problematic and unfair, but it becomes an issue of great concern when the unfairness isn’t applied fairly.

Shiori is preparing a civil suit against Mr. Yamaguchi as well. Her lawyers point to a successful case last March where a civil court ruled in favor of a rape victim. The case, a rare victory for sexual assault victims, involved a then-26-year-old woman who was allegedly drugged then raped by her colleagues in 2011. The woman filed a complaint with the police immediately after the alleged assault, but investigators sat on the case for more than four years, forcing the victim to turn to civil court.

“This case was an important precedent because many victims think that because they don’t remember (the assault) they have no recourse,” said Dr. Chieko Nagai, who treated the plaintiff and provided medical testimony in her civil case. Nagai, who runs a small medical clinic in Tokyo, said she sees parallels in the 2016 case with that of Shiori. She notes Japanese police and medical institutions fail victims by not running blood and urine tests immediately after an alleged attack to determine if victims were drugged.

Lawyers and advocates say sexual assault victims would not have to turn to civil courts if criminal cases were properly investigated. Women forced to seek relief in civil courts because of failures in the penal system are similar to victims of Japan’s organized crime groups, the yakuza. Police sometimes fail to pin murder cases on yakuza bosses, mostly because prosecutors flinch at taking anything but slam-dunk cases, but the families of the deceased can sue the top bosses in civil court for damages under the guise of “employer liability.” They usually win and thus the yakuza will now often settle out of court.

Shiori has asked the Prosecutorial Review Board to rule for prosecution in her case. Her odds of winning such a decision are roughly 1 percent. And even if the first decision goes in her favor, the prosecution may still refuse to indict again.

Her lawyer says, “I know the odds are against us but I believe that an objective review of the evidence we have collected by a disinterested third party will result in justice being done and the case being tried in court, not being discarded at the front door.”

Even if Shiori wins nothing in her own case, she has helped make a remarkable thing come true for Japanese women—the first major revisions of the sexual assault laws in over a hundred years.

The audacity of her two sentences of criticism earned her jeers as “a left-wing plant” from Japan’s cyber trolls but it also reminded the public that the sexual assault of women in this country has continued with impunity for far too long.

Despite everything, her efforts were not in vain. Shiori informed us, in a short message written in English, “On the last day of the Diet session [last Friday] I received a message from the Diet Affairs Committee Chairman that they changed the laws on rape in the last day. And he thanked me. :) it is a small step but I’m so happy!”